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PAPER → GALAXY

Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.

draft pipelinesource/papertarget/galaxy

Phases

/ subway map 13 phases
  1. summarize-paper
  2. paper-summary-to-galaxy-design
  3. compare-against-iwc-exemplar
  4. paper-summary-to-galaxy-template
  5. branch discover-or-author loop
  6. summarize-galaxy-tool loop
  7. implement-galaxy-tool-step loop
  8. validate-galaxy-step loop
  9. branch test-data-resolution
    1. paper-to-test-data
    2. find-test-data
    3. user-supplied
  10. implement-galaxy-workflow-test
  11. validate-galaxy-workflow
  12. run-workflow-test
  13. debug-galaxy-workflow-output

PAPER → GALAXY

Direct path. Lifted from docs/HARNESS_PIPELINES.md §“PAPER → GALAXY”.

The composed alternative PAPER → CWL → GALAXY is a runtime composition of paper-to-cwl followed by cwl-to-galaxy — open question whether to surface as a distinct pipeline note.